Article
Nanoscience & Nanotechnology
Danni Chen, Heng Li, Bin Yu, Junle Qu
Summary: This study proposes a method for researching dynamic events in living cells by simultaneously monitoring spatial positions and changes in local environment related to fluorescence lifetime. The feasibility of the method is verified through experiments, and intracellular endocytosis in a living cell is successfully observed.
Article
Biochemical Research Methods
Francois Laurent, Hippolyte Verdier, Maxime Duval, Alexander Serov, Christian L. Vestergaard, Jean-Baptiste Masson
Summary: Single-molecule localization microscopy is an important tool for studying the dynamics and cellular function of biomolecules. We introduce TRamWAy, a modular Python library that provides various functions including data tracking, meshing, inverse model solving, and analysis, along with a simple web-based interface.
Article
Biochemical Research Methods
Laura Perez-Garcia, Martin Selin, Antonio Ciarlo, Alessandro Magazzu, Giuseppe Pesce, Antonio Sasso, Giovanni Volpe, Isaac Perez Castillo, Alejandro V. Arzola
Summary: Optical tweezers are essential tools in physics, chemistry, and biology for precise micromanipulation and force measurement. This study presents a general approach based on sampled trajectories to accurately estimate the trap stiffness and diffusion constant of optically trapped particles by correcting for the biases caused by finite integration time and limited sampling frequency.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Optics
Guolong Chen, Youlin Gu, Yihua Hu, Fanhao Meng, Wanying Ding, Xi Zhang
Summary: This study presents a method to accurately determine the extinction characteristics of non-spherical biological particle aggregates. A randomly oriented aggregation model was constructed based on the multi-sphere particle model. The extinction characteristics of aggregates in the 3-14 μm waveband were calculated using the discrete-dipole approximation method. Experimental results from a smoke chamber support the theoretical analyses.
CHINESE OPTICS LETTERS
(2023)
Article
Multidisciplinary Sciences
Jan N. Hansen, An Gong, Dagmar Wachten, Rene Pascal, Alex Turpin, Jan F. Jikeli, U. Benjamin Kaupp, Luis Alvarez
Summary: The authors present an open-source 3D reconstruction algorithm for label-free tracking of spherical and filamentous structures using multifocal imaging, which they use to characterize fluid flow and flagellar beating of human and sea urchin sperm.
NATURE COMMUNICATIONS
(2021)
Article
Mechanics
Zhe Zuo, Tingting Fang, Hao Wu, Zhenyu Zhang
Summary: In this study, deep learning models are developed to estimate the three-dimensional velocity fields produced by the atomization process of two impinging jets. The models are trained using a dataset generated by direct numerical simulations, and they show promising results in accurately reconstructing volume velocity data from two-dimensional images.
Article
Multidisciplinary Sciences
Chao Jiang, Mingcheng Yang, Wei Li, Shuo-Xing Dou, Peng-Ye Wang, Hui Li
Summary: Intracellular transport, regulated by complex cytoarchitectures and active driving forces, plays a crucial role in biomolecule translocations and cellular functions. This study utilized 3D single-particle tracking to investigate the dynamics of intracellular transport. The results showed that the transport changes from thermal-dominated 3D-constrained motion to active-dominated quasi-2D motion, with heterogeneous lateral motion and homogeneous axial motion. The anisotropy and heterogeneity of vesicle transport were found to be due to actively directed motion on microtubules. Moreover, it was observed that endocytic cargos make diffusive motions on the inner vesicle membranes, suggesting a physical connection to microtubules during transport.
Article
Chemistry, Multidisciplinary
Guangzhong Ma, Zijian Wan, Yunze Yang, Wenwen Jing, Shaopeng Wang
Summary: This study introduces a plasmonic imaging technique that enables precise 3D tracking of surface-tethered single particles in real time, with applications in studying DNA-enzyme interactions. The analysis of particle motion patterns allows for the identification of specific and nonspecific interactions in immunoassays, contributing to the understanding of molecular dynamics and interactions at the single-molecule level.
Article
Biology
Alec Heckert, Liza Dahal, Robert Tijan, Xavier Darzacq
Summary: Single-particle tracking (SPT) is a powerful tool for studying molecular mechanisms of cellular regulation. However, there are technical limitations in interpreting SPT data for fast-diffusing proteins. Researchers have proposed methods based on Bayesian nonparametrics to address these limitations.
Article
Engineering, Multidisciplinary
Masami Matsubara, Takeru Wako, Tsuneyoshi Matsuoka, Shozo Kawamura
Summary: A novel digital image displacement measurement system using the PASTA method is proposed, which tracks subsets in the x-and y-directions coupled with double circular markers. The method achieves subpixel resolution by analyzing the luminance differences of subsets. Numerical simulations and experiments verify the validity and robustness of the method.
PRECISION ENGINEERING-JOURNAL OF THE INTERNATIONAL SOCIETIES FOR PRECISION ENGINEERING AND NANOTECHNOLOGY
(2022)
Article
Engineering, Multidisciplinary
Massimiliano Rossi, Rune Barnkob
Summary: The increasing use of microfluidics in industrial, biomedical, and clinical applications requires more precise control of microfluidic flows and suspended particles or cells, leading to higher demands in three-dimensional and automated particle tracking methods. General defocusing particle tracking (GDPT) is a versatile approach suitable for different types of images, with fast and segmentation-free features, suitable for automated and real-time applications.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2021)
Article
Physics, Multidisciplinary
Konstantin Speckner, Matthias Weiss
Summary: Single-particle tracking is a powerful tool for quantifying transport phenomena in complex media, allowing for detailed comparison with theoretical predictions. When applied to biochemically active cell extracts, it reveals key insights into the transport behavior of nano-sized particles.
Article
Chemistry, Multidisciplinary
Nadav Opatovski, Yael Shalev Ezra, Lucien E. Weiss, Boris Ferdman, Reut Orange-Kedem, Yoav Shechtman
Summary: The study introduces a novel method for efficient multicolor 3D particle tracking over a large field of view, achieved through multiplexed point-spread-function engineering. The technique has been successfully demonstrated for tracking five types of emitters in vitro and colocalization of DNA loci in live yeast cells.
Article
Physics, Fluids & Plasmas
Lei Fang, Nicholas T. Ouellette
Summary: Researchers found that although flow patterns consistent with previous claims of spectral condensation exist in two-dimensional flows, no signatures were observed in the energy spectrum. Their study suggests that small domains weaken the turbulent cascade, which requires stronger evidence to support claims of condensation.
PHYSICAL REVIEW FLUIDS
(2021)
Article
Biochemical Research Methods
Zhuo Wang, Gao Chen, Shuanglian Wang, Xuantao Su
Summary: This article presents a three-dimensional deep regression-based light scattering imaging system for nanoparticle analysis. The system overcomes the problem of object focusing in common methods and can obtain light scattering images of label-free nanoparticles as small as 41 nm in diameter. Exosomes from normal and cancer liver cells can be observed and automatically differentiated using this system. The 3D deep regression-based light scattering imaging system is expected to be widely utilized in the field of nanoparticle analysis and nanomedicine.
BIOMEDICAL OPTICS EXPRESS
(2023)
Article
Chemistry, Multidisciplinary
Andreas Neophytou, Vinothan N. Manoharan, Dwaipayan Chakrabarti
Summary: Through a computational approach, we address the challenges of design principles, self-assembly pathways, and stability of the photonic band gap. We establish the design principles for the rod-connected diamond structure (RCD) and devise two distinct self-assembly routes, showing how these routes avoid metastable amorphous phases. Finally, we demonstrate that both polymorphs support spectrally overlapping photonic band gaps.
Article
Multidisciplinary Sciences
Victoria Hwang, Anna B. Stephenson, Solomon Barkley, Soeren Brandt, Ming Xiao, Joanna Aizenberg, Vinothan N. Manoharan
Summary: Disordered nanostructures can exhibit angle-independent structural colors, potentially replacing dyes in some applications. Designing specific colors in nanostructures is challenging, but can be achieved through modeling and optimization approaches. Developing accurate predictive models for disordered nanostructures with multiple scattering is key to engineering design of structural colors for various applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Optics
Caroline Martin, Brian Leahy, Vinothan N. Manoharan
Summary: This study investigates the effects of spherical aberration on single-particle holograms and accuracy of particle characterization, finding that it can lead to systematic shifts in inferred refractive index and radius. Fitting with a model that considers spherical aberration can reduce this error significantly, making particle characterization more robust across different levels of aberration.
Article
Optics
Ming Xiao, Anna B. Stephenson, Andreas Neophytou, Victoria Hwang, Dwaipayan Chakrabarti, Vinothan N. Manoharan
Summary: Photonic glasses, isotropic structures with short-range correlations, can produce structural colors with little angle-dependence, though this may result in low color saturation. The trade-off between saturation and angle-independence can be broken by tuning the width of the first peak of the structure factor and controlling sample thickness. The protocol used to pack particles into a photonic glass is crucial for its optical properties.
Article
Nanoscience & Nanotechnology
Nabila Tanjeem, William H. Wilkin, Daniel A. Beller, Chris H. Rycroft, Vinothan N. Manoharan
Summary: This study investigates the growth of 2D crystals of colloidal nanoparticles on cylindrical substrates using a combination of experiment and simulation. The cylindrical geometry influences how the crystals grow, resulting in kinked line slips containing partial vacancies. The closure constraint of the cylinder leads to frustrated crystal growth, impacting the formation of structures such as chiral optical nanomaterials.
ACS APPLIED NANO MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Emily W. Gehrels, W. Benjamin Rogers, Zorana Zeravcic, Vinothan N. Manoharan
Summary: By functionalizing colloidal particles with DNA oligonucleotides, they can be programmed to interact in complex ways and respond to temperature changes using DNA strand-displacement reactions. This study explores the requirements for thermally driven directed motion of colloidal particles and demonstrates the design considerations and limitations of using DNA-mediated interactions in dynamic systems.
Article
Multidisciplinary Sciences
Cheng Zeng, Maya Winters Faaborg, Ahmed Sherif, Martin J. Falk, Rozhin Hajian, Ming Xiao, Kara Hartig, Yohai Bar-Sinai, Michael P. Brenner, Vinothan N. Manoharan
Summary: In this study, capillary forces are dynamically modulated to move objects in programmable two-dimensional patterns. Machines are designed to translate, rotate, separate, and braid multiple floating objects. This approach provides a quick, inexpensive way to manipulate micrometre-scale particles and braid microwires for high-frequency electronics.
Article
Nanoscience & Nanotechnology
Anna B. Stephenson, Ming Xiao, Victoria Hwang, Liangliang Qu, Paul A. Odorisio, Michael Burke, Keith Task, Ted Deisenroth, Solomon Barkley, Rupa H. Darji, Vinothan N. Manoharan
Summary: Photonic balls are spheres that contain nanoparticles or nanopores, with a diameter comparable to the wavelength of light. They can exhibit structural color due to their disordered but correlated nanoscale features, making them a promising type of pigment for various applications. However, predicting the color of materials made from photonic balls is challenging due to the need to account for sphere geometry and multiple scattering. In this study, a multiscale modeling approach involving Monte Carlo simulations is developed to address these challenges.
Article
Education, Scientific Disciplines
Jerome Fung, Christopher L. Weil
Summary: We use the inexpensive microcontroller Teensy 3.5 for phase-sensitive detection, which offers superior hardware performance compared to commonly used Arduino microcontrollers. Our Teensy-based detector can operate with external or internally generated reference signals, and we have developed a open-source graphical user interface for controlling the instrument. Our phase-sensitive detector exhibits good linearity in amplitude and phase, and can be a low-cost alternative to commercial lock-in amplifiers for teaching and laboratory measurements.
AMERICAN JOURNAL OF PHYSICS
(2023)
Article
Optics
Xander M. De Wit, Amelia W. Paine, Caroline Martin, Aaron M. Goldfain, Rees F. Garmann, Vinothan N. Manoharan
Summary: Interferometric scattering microscopy combined with Bayesian framework and automatic differentiation technique presents a new method for analyzing interferometric images, enabling the determination of three-dimensional position, polarizability, uncertainties, and correlations of nanoscale systems, as well as inferring their static and dynamic properties.
Article
Chemistry, Physical
Clary Rodriguez-Cruz, Mehdi Molaei, Amruthesh Thirumalaiswamy, Klebert Feitosa, Vinothan N. Manoharan, Shankar Sivarajan, Daniel H. Reich, Robert A. Riggleman, John C. Crocker
Summary: A recent study showed that the random motions of the bubbles in a soft glassy material are due to the configuration of the system moving over a fractal energy landscape in high-dimensional space. The analysis of the observed trajectories of oil droplets in a dense emulsion reproduced the high-dimensional fractal geometry of the configuration path and confirmed the presence of fractal energy landscape dynamics. This discovery suggests that similar dynamics in different soft and biological materials may also be attributed to fractal landscape dynamics.
Review
Multidisciplinary Sciences
Caroline Martin, Lauren E. Altman, Siddharth Rawat, Anna Wang, David G. Grier, Vinothan N. Manoharan
Summary: Holographic microscopy is an optical microscope that collects holograms and analyzes them to obtain information about specimen properties. It offers high-speed acquisition of precise results. This Primer introduces in-line holographic microscopy and three analysis methods and discusses applications, reproducibility, and limitations. It also provides an outlook on future development and the integration between experiment and computational analysis.
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Chemistry, Multidisciplinary
Ming Xiao, Jie Mao, Matthias Kollosche, Victoria Hwang, David R. Clarke, Vinothan N. Manoharan
Summary: Structurally colored materials have the potential to switch colors in response to external stimuli, making them useful in various applications. However, their use is restricted by angular dependence, slow response, and lack of synchronous control. To address these challenges, the combination of structurally colored photonic glasses and elastomer actuators provides a solution with quick color changes and instability tolerance. This platform can be applied in soft and curved color displays, camouflage, and multifunctional sensors.
MATERIALS HORIZONS
(2022)
Meeting Abstract
Biophysics
Ofer Kimchi, Rees Garmann, Timothy Chiang, Megan Engel, Michael P. Brenner, Vinothan N. Manoharan
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Nabila Tanjeem, Cyril Chomette, Nicholas B. Schade, Serge Ravaine, Etienne Duguet, Mona Treguer-Delapierre, Vinothan N. Manoharan
Summary: A new approach to making plasmonic metamolecules with well-controlled resonances at optical wavelengths is described, utilizing a multi-step colloidal synthesis method to achieve nanometer-scale precision in morphology. Using single-cluster spectroscopy, it is shown that the plasmonic resonances are reproducible from cluster to cluster. By comparing the spectra to theory, the multi-step synthesis approach is demonstrated to control the distances between metallic surfaces with nanometer-scale precision.
MATERIALS HORIZONS
(2021)